Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment.
Autorzy:
Talebi S; University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA. Tong E; Stanford University, Stanford, CA, USA. Li A; Stanford University, Stanford, CA, USA. Yamin G; Stanford University, Stanford, CA, USA. Zaharchuk G; Stanford University, Stanford, CA, USA. MofradMRK; University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA. mofrad@berkeley.edu.
Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation.
Autorzy:
Zamri MHB; Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan. Ujihara Y; Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan. Nakamura M; Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan.; Center of Biomedical Physics and Information Technology, Nagoya Institute of Technology, Nagoya 466-8555, Japan.; Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Graduate School of Engineering, Nagoya 466-8555, Japan. MofradMRK; Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA. Sugita S; Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, School of Engineering, Nagoya 466-8555, Japan.; Center of Biomedical Physics and Information Technology, Nagoya Institute of Technology, Nagoya 466-8555, Japan.
Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex.
Autorzy:
Lennon KM; Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA. Soheilypour M; Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA. Peyro M; Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA. Wakefield DL; Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA. Choo GE; Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA. MofradMRK; Department of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California, Berkeley, CA 94720, USA.; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Jovanovic-Talisman T; Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
Atomic Scale Interactions between RNA and DNA Aptamers with the TNF- α Protein.
Autorzy:
Asadzadeh H; Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11365-9567, Tehran 11365-9567, Iran. Moosavi A; Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Azadi Avenue, P.O. Box 11365-9567, Tehran 11365-9567, Iran. Alexandrakis G; Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA. MofradMRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, USA.
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Źródło:
BioMed research international [Biomed Res Int] 2021 Jul 16; Vol. 2021, pp. 9926128. Date of Electronic Publication: 2021 Jul 16 (Print Publication: 2021).
PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks.
Autorzy:
Seyyedsalehi SF; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.; Department of Mechanical Engineering, University of California Berkeley, Berkeley, California, United States of America. Soleymani M; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. Rabiee HR; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. MofradMRK; Department of Mechanical Engineering, University of California Berkeley, Berkeley, California, United States of America.
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Źródło:
PloS one [PLoS One] 2021 Feb 25; Vol. 16 (2), pp. e0244430. Date of Electronic Publication: 2021 Feb 25 (Print Publication: 2021).
Typ publikacji:
Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain.
Autorzy:
Didonna A; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Damotte V; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Shams H; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Matsunaga A; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Caillier SJ; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Dandekar R; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Misra MK; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.; Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA. MofradMRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, USA.; Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA. Oksenberg JR; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. Hollenbach JA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
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Źródło:
Immunology [Immunology] 2021 Feb; Vol. 162 (2), pp. 194-207. Date of Electronic Publication: 2020 Oct 19.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Machine learning for endoleak detection after endovascular aortic repair.
Autorzy:
Talebi S; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA. Madani MH; Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA. Madani A; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA.; Salesforce Research, Palo Alto, CA, USA. Chien A; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA. Shen J; Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA. Mastrodicasa D; Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA. Fleischmann D; Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA. Chan FP; Department of Radiology, School of Medicine, Stanford University, Stanford, CA, USA. . MofradMRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, 208A Stanley Hall #1762, Berkeley, CA, 94720-1762, USA. mofrad@berkeley.edu.; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. mofrad@berkeley.edu.
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Źródło:
Scientific reports [Sci Rep] 2020 Oct 27; Vol. 10 (1), pp. 18343. Date of Electronic Publication: 2020 Oct 27.
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX).
Autorzy:
Asgari E; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, 94720, USA.; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, 38124, Germany. McHardy AC; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, 38124, Germany. MofradMRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, 94720, USA. mofrad@berkeley.edu.; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA. mofrad@berkeley.edu.
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Źródło:
Scientific reports [Sci Rep] 2019 Mar 05; Vol. 9 (1), pp. 3577. Date of Electronic Publication: 2019 Mar 05.
Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system.
Autorzy:
Soheilypour M; a Molecular Cell Biomechanics Laboratory , Departments of Bioengineering and Mechanical Engineering, University of California , Berkeley. MofradMRK; a Molecular Cell Biomechanics Laboratory , Departments of Bioengineering and Mechanical Engineering, University of California , Berkeley.
Mechanical Contact Characteristics of PC3 Human Prostate Cancer Cells on Complex-Shaped Silicon Micropillars.
Autorzy:
Seo BB; Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. . Jahed Z; Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, 208A Stanley Hall, Berkeley, CA 94720, USA. . Coggan JA; Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. . Chau YY; Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. . Rogowski JL; Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. . Gu FX; Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. . Wen W; Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. . MofradMRK; Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, 208A Stanley Hall, Berkeley, CA 94720, USA. mofrad@berkeley.edu. Tsui TY; Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. .
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Źródło:
Materials (Basel, Switzerland) [Materials (Basel)] 2017 Aug 02; Vol. 10 (8). Date of Electronic Publication: 2017 Aug 02.
Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen.
Autorzy:
Madani A; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America. Garakani K; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America. MofradMRK; Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America.; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America.
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Źródło:
PloS one [PLoS One] 2017 Jun 30; Vol. 12 (6), pp. e0179601. Date of Electronic Publication: 2017 Jun 30 (Print Publication: 2017).
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